1kbb - Revision history

OCA at 07:59, 3 April 2024

OCA — Wed, 03 Apr 2024 07:59:03 GMT

←Older revision		Revision as of 07:59, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='1kbb' size='340' side='right'caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1kbb' size='340' side='right'caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KBB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KBB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~PCA~~:~~PYROGLUTAMIC~~+~~ACID~~'>~~PCA~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [https://pdbe.org/1kbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [https://www.ebi.ac.uk/pdbsum/1kbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kbb ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [https://pdbe.org/1kbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [https://www.ebi.ac.uk/pdbsum/1kbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kbb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AMYP_HUMAN AMYP_HUMAN]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kbb ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kbb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The roles of three conserved active site carboxylic acids (D197, E233, and D300) in the catalytic mechanism of human pancreatic alpha-amylase (HPA) were studied by utilizing site-directed mutagenesis in combination with structural and kinetic analyses of the resultant enzymes. All three residues were mutated to both alanine and the respective amide, and a double alanine mutant (E233A/D300A) was also generated. Structural analyses demonstrated that there were no significant differences in global fold for the mutant enzymes. Kinetic analyses were performed on the mutants, utilizing a range of substrates. All results suggested that D197 was the nucleophile, as virtually all activity (>10(5)-fold decrease in k(cat) values) was lost for the enzymes mutated at this position when assayed with several substrates. The significantly greater second-order rate constant of E233 mutants on "activated" substrates (k(cat)/K(m) value for alpha-maltotriosyl fluoride = 15 s(-)(1) mM(-)(1)) compared with "unactivated" substrates (k(cat)/K(m) value for maltopentaose = 0.0030 s(-)(1) mM(-)(1)) strongly suggested that E233 is the general acid catalyst, as did the pH-activity profiles. Transglycosylation was favored over hydrolysis for the reactions of several of the enzymes mutated at D300. At the least, this suggests an overall impairment of the catalytic mechanism where the reaction then proceeds using the better acceptor (oligosaccharide instead of water). This may also suggest that D300 plays a crucial role in enzymic interactions with the nucleophilic water during the hydrolysis of the glycosidic bond.
-
-	Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids.,Rydberg EH, Li C, Maurus R, Overall CM, Brayer GD, Withers SG Biochemistry. 2002 Apr 2;41(13):4492-502. PMID:11914097<ref>PMID:11914097</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kbb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Amylase 3D structures\|Amylase 3D structures]]		*[[Amylase 3D structures\|Amylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alpha-amylase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brayer~~, G D~~]]	+	[[Category: Brayer GD]]
-	[[Category: Li, C]]	+	[[Category: Li C]]
-	[[Category: Maurus, R]]	+	[[Category: Maurus R]]
-	[[Category: Overall~~, C M~~]]	+	[[Category: Overall CM]]
-	[[Category: Rydberg~~, E H~~]]	+	[[Category: Rydberg EH]]
-	[[Category: Withers~~, S G]]~~	+	[[Category: Withers SG]]
-	~~[[Category: Amylase]]~~	+
-	~~[[Category: Carbohydrate metabolism]]~~	+
-	~~[[Category: Catalysis]]~~	+
-	~~[[Category: Diabetes]]~~	+
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Glycosylation]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mutagenesis]]~~	+
-	~~[[Category: Pancreatic~~]]	+

OCA at 09:19, 29 September 2021

OCA — Wed, 29 Sep 2021 09:19:39 GMT

←Older revision		Revision as of 09:19, 29 September 2021
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	<StructureSection load='1kbb' size='340' side='right'caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1kbb' size='340' side='right'caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KBB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KBB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [~~http~~://pdbe.org/1kbb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kbb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kbb ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [https://pdbe.org/1kbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [https://www.ebi.ac.uk/pdbsum/1kbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kbb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 13:18, 17 July 2019

OCA — Wed, 17 Jul 2019 13:18:26 GMT

←Older revision		Revision as of 13:18, 17 July 2019
Line 1:		Line 1:

	==Mechanistic Analyses of Catalysis in Human Pancreatic alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids==		==Mechanistic Analyses of Catalysis in Human Pancreatic alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids==
-	<StructureSection load='1kbb' size='340' side='right' caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1kbb' size='340' side='right'caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KBB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KBB FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/1kbb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/1kbb_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1kbb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kbb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Amylase 3D structures\|Amylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Brayer, G D]]		[[Category: Brayer, G D]]
	[[Category: Li, C]]		[[Category: Li, C]]

OCA at 07:32, 11 October 2017

OCA — Wed, 11 Oct 2017 07:32:42 GMT

←Older revision		Revision as of 07:32, 11 October 2017
Line 1:		Line 1:
		+
	==Mechanistic Analyses of Catalysis in Human Pancreatic alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids==		==Mechanistic Analyses of Catalysis in Human Pancreatic alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids==
	<StructureSection load='1kbb' size='340' side='right' caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1kbb' size='340' side='right' caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [http://pdbe.org/1kbb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [http://www.ebi.ac.uk/pdbsum/1kbb PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [http://pdbe.org/1kbb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [http://www.ebi.ac.uk/pdbsum/1kbb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kbb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kbb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1kbb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kbb" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Amylase\|Amylase]]
-	*[[User:Gabriel Pons/Sandbox 2\|User:Gabriel Pons/Sandbox 2]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:46, 11 September 2015

OCA — Fri, 11 Sep 2015 07:46:28 GMT

←Older revision		Revision as of 07:46, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1kbb' size='340' side='right' caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1kbb' size='340' side='right' caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KBB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KBB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [http://www.ebi.ac.uk/pdbsum/1kbb PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [http://pdbe.org/1kbb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [http://www.ebi.ac.uk/pdbsum/1kbb PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1kbb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Brayer, G D]]		[[Category: Brayer, G D]]
	[[Category: Li, C]]		[[Category: Li, C]]
Line 49:		Line 50:
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Glycosylation]]		[[Category: Glycosylation]]
-	[[Category: Human]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Mutagenesis]]		[[Category: Mutagenesis]]
	[[Category: Pancreatic]]		[[Category: Pancreatic]]

OCA at 15:45, 5 January 2015

OCA — Mon, 05 Jan 2015 15:45:45 GMT

←Older revision		Revision as of 15:45, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KBB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KBB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [http://www.ebi.ac.uk/pdbsum/1kbb PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [http://www.ebi.ac.uk/pdbsum/1kbb PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	==See Also==		==See Also==
	*[[Amylase\|Amylase]]		*[[Amylase\|Amylase]]
		+	*[[User:Gabriel Pons/Sandbox 2\|User:Gabriel Pons/Sandbox 2]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 36:
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Brayer, G D.]]	+	[[Category: Brayer, G D]]
-	[[Category: Li, C.]]	+	[[Category: Li, C]]
-	[[Category: Maurus, R.]]	+	[[Category: Maurus, R]]
-	[[Category: Overall, C M.]]	+	[[Category: Overall, C M]]
-	[[Category: Rydberg, E H.]]	+	[[Category: Rydberg, E H]]
-	[[Category: Withers, S G.]]	+	[[Category: Withers, S G]]
	[[Category: Amylase]]		[[Category: Amylase]]
	[[Category: Carbohydrate metabolism]]		[[Category: Carbohydrate metabolism]]

OCA at 11:57, 28 September 2014

OCA — Sun, 28 Sep 2014 11:57:02 GMT

←Older revision		Revision as of 11:57, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1kbb.~~png~~\|~~left~~\|200px]]	+	==Mechanistic Analyses of Catalysis in Human Pancreatic alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids==
		+	<StructureSection load='1kbb' size='340' side='right' caption='[[1kbb]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kbb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KBB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kbb RCSB], [http://www.ebi.ac.uk/pdbsum/1kbb PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/1kbb_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The roles of three conserved active site carboxylic acids (D197, E233, and D300) in the catalytic mechanism of human pancreatic alpha-amylase (HPA) were studied by utilizing site-directed mutagenesis in combination with structural and kinetic analyses of the resultant enzymes. All three residues were mutated to both alanine and the respective amide, and a double alanine mutant (E233A/D300A) was also generated. Structural analyses demonstrated that there were no significant differences in global fold for the mutant enzymes. Kinetic analyses were performed on the mutants, utilizing a range of substrates. All results suggested that D197 was the nucleophile, as virtually all activity (>10(5)-fold decrease in k(cat) values) was lost for the enzymes mutated at this position when assayed with several substrates. The significantly greater second-order rate constant of E233 mutants on "activated" substrates (k(cat)/K(m) value for alpha-maltotriosyl fluoride = 15 s(-)(1) mM(-)(1)) compared with "unactivated" substrates (k(cat)/K(m) value for maltopentaose = 0.0030 s(-)(1) mM(-)(1)) strongly suggested that E233 is the general acid catalyst, as did the pH-activity profiles. Transglycosylation was favored over hydrolysis for the reactions of several of the enzymes mutated at D300. At the least, this suggests an overall impairment of the catalytic mechanism where the reaction then proceeds using the better acceptor (oligosaccharide instead of water). This may also suggest that D300 plays a crucial role in enzymic interactions with the nucleophilic water during the hydrolysis of the glycosidic bond.

-	~~{{STRUCTURE_1kbb\| PDB=1kbb \| SCENE= }}~~	+	Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids.,Rydberg EH, Li C, Maurus R, Overall CM, Brayer GD, Withers SG Biochemistry. 2002 Apr 2;41(13):4492-502. PMID:11914097<ref>PMID:11914097</ref>

-	~~===Mechanistic Analyses~~ of ~~Catalysis in Human Pancreatic alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11914097}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1kbb]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Alpha-~~Amylase\|~~Alpha-~~Amylase]]	+	*[[Amylase\|Amylase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011914097<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 17:13, 20 October 2012

OCA — Sat, 20 Oct 2012 17:13:03 GMT

←Older revision		Revision as of 17:13, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1kbb]] is a 1 chain structure ~~of [[Alpha-Amylase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA].	+	[[1kbb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA].

	==See Also==		==See Also==

OCA: Protected "1kbb" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 00:12:26 GMT

Protected "1kbb" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:12, 27 July 2012

OCA at 00:12, 27 July 2012

OCA — Fri, 27 Jul 2012 00:12:24 GMT

←Older revision		Revision as of 00:12, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1kbb.png\|left\|200px]]		[[Image:1kbb.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1kbb", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1kbb\| PDB=1kbb \| SCENE= }}		{{STRUCTURE_1kbb\| PDB=1kbb \| SCENE= }}

	===Mechanistic Analyses of Catalysis in Human Pancreatic alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids===		===Mechanistic Analyses of Catalysis in Human Pancreatic alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11914097}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11914097 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11914097}}		{{ABSTRACT_PUBMED_11914097}}

	==About this Structure==		==About this Structure==
-	~~1KBB~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA].	+	[[1kbb]] is a 1 chain structure of [[Alpha-Amylase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBB OCA].
		+
		+	==See Also==
		+	*[[Alpha-Amylase\|Alpha-Amylase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11914097~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011914097</ref><references group="xtra"/>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
Line 43:		Line 34:
	[[Category: Mutagenesis]]		[[Category: Mutagenesis]]
	[[Category: Pancreatic]]		[[Category: Pancreatic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:22:01 2009''